diff pathview.r @ 0:bd99e8fbde97 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pathview.r	Mon Aug 26 14:42:52 2019 -0400
@@ -0,0 +1,89 @@
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("pathview")
+    library("optparse")
+})
+
+sessionInfo()
+
+option_list <- list(
+  make_option(c("--pathway_id"), type="character", default=NULL, help="Path to tabular file with gene data"),
+  make_option(c("--pathway_id_fp"), type="character", default=NULL, help="Path to tabular file with pathway ids"),
+  make_option(c("--pathway_id_header"), type="logical", default=FALSE, help="Header for tabular file with pathway ids"),
+  make_option(c("--species"), type="character", default="hsa", help="KEGG code, scientific name or the common name of the species"),
+  make_option(c("--gene_data"), type="character", default=NULL, help="Path to tabular file with gene data"),
+  make_option(c("--gd_header"), type="logical", default=FALSE, help="Header for the gene data file"),
+  make_option(c("--gene_idtype"), type="character", default="entrez", help="ID type used for the gene data"),
+  make_option(c("--cpd_data"), type="character", default=NULL, help="Path to tabular file with compound data"),
+  make_option(c("--cpd_header"), type="logical", default=FALSE, help="Header for the compound data file"),
+  make_option(c("--cpd_idtype"), type="character", default="kegg", help="ID type used for the compound data"),
+  make_option(c("--multi_state"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
+  make_option(c("--match_data"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
+  make_option(c("--kegg_native"), type="logical", default=TRUE, help="Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
+  make_option(c("--same_layer"), type="logical", default=TRUE, help="Plot on same layer?"),
+  make_option(c("--map_null"), type="logical", default=TRUE, help="Map the NULL gene or compound data to pathway?"),
+  make_option(c("--split_group"), type="logical", default=FALSE, help="Split node groups into individual nodes?"),
+  make_option(c("--expand_node"), type="logical", default=FALSE, help="Expand multiple-gene nodes into single-gene nodes?"),
+  make_option(c("--sign_pos"), type="character", default="bottomright", help="Position of pathview signature")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+print(args)
+
+read_table = function(fp, header, rownames=1, colclasses=NA){
+  table = read.table(fp, header=header, sep="\t", row.names=rownames, colClasses=colclasses)
+  # transform to vector if only one column
+  if(dim(table)[2] == 1){
+    names = rownames(table)
+    table = table[,1]
+    names(table) = names
+  }
+  return(table)
+}
+
+get_table = function(fp, header){
+  table = NULL
+  if(!is.null(fp)){
+    table = read_table(fp, header, rownames=1)
+  }
+  return(table)
+}
+
+# load gene_data file
+gene_data = get_table(args$gene_data, args$gd_header)
+
+# load compound data file
+cpd_data = get_table(args$cpd_data, args$cpd_header)
+
+run_pathview = function(pathway_id){
+  pathview(
+    pathway.id=pathway_id,
+    gene.data=gene_data,
+    gene.idtype=args$gene_idtype,
+    cpd.data=cpd_data,
+    cpd.idtype=args$cpd_idtype,
+    species=args$species,
+    multi.state=args$multi_state,
+    match.data=args$match_data,
+    kegg.native=args$kegg_native,
+    same.layer=args$same_layer,
+    split.group=args$split_group,
+    expand.node=args$expand_node,
+    sign.pos=args$sign_pos,
+    map.null=args$map_null)
+}
+
+# get pathway ids
+if(!is.null(args$pathway_id)){
+  run_pathview(args$pathway_id)
+} else {
+  pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character")
+  for(p in pthws){
+    run_pathview(p)
+  }
+}